HDAC9 p.Pro338=
c.1014C>T · VCV3524485
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -5.2 |
| Overall | ||
| CADD | 5.995 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/90,842 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.000822%
12/1,459,470 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,421 |
| European (non-Finnish) | 0.000848% | 117,869 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- HDAC9
- Protein
- p.Pro338=
- Coding
- c.1014C>T
- MANE Select
- NM_178425
- Type
- single nucleotide variant
- Location
- chr7:18644772 (GRCh38)
- Gene constraint
- LOEUF 0.377 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.48 · 2 PDB
- Residue 338
- the 'interaction with mapk10' region
Similar variants
- HDAC9 p.Pro390= Benign ★★ same type
- HDAC9 c.1910-2A>G Uncertain significance ★ same type
- HDAC9 p.Ala1028Val Uncertain significance ★ same type
- HDAC9 p.Ala1068Val Uncertain significance ★ same type
- HDAC9 p.Ala140Ser Uncertain significance ★ ⚠ same type
- HDAC9 p.Ala238Thr Uncertain significance ★ ⚠ same type
- HDAC9 p.Ala339Ser Uncertain significance ★ ⚠ same type
- HDAC9 p.Ala346Thr Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/hdac9-p-pro338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown